Figure 233. Clustered heatmap of normalized abundance values. Number of cluster splits is determined automatically with method fpc::pamk. Image file: 
plots/32341ce43f8.svg. 
noone@mail.com Analysis of Dieting study 16S data % Fri Sep 7 05:46:18 2018
Filtering abundance matrix with arguments [ min_mean :10, min_quant_incidence_frac:0.25, min_quant_mean_frac :0.25]. Filtering features
Note that some community richness estimators will not work correctly if provided with abundance-filtered counts
After filtering, left 87 records for 120 features
Wrote counts and metadata for raw counts After final feature filtering to files data/1.1.1.4.2.1-32378e5b444samples.raw.16s.l.otu.count.tsv,data/1.1.1.4.2.1-32378e5b444samples.raw.16s.l.otu.attr.tsv
Wrote counts and metadata for proportions counts After final feature filtering to files data/1.1.1.4.2.1-3234be14d9dsamples.proportions.16s.l.otu.count.tsv,data/1.1.1.4.2.1-3234be14d9dsamples.proportions.16s.l.otu.attr.tsv
Specific methods can override these and use their own normalization.
Count normalization method for data analysis (unless modified by specific methods) : [ drop.features:List of 1, ..$ :"other", method.args :List of 1, ..$ theta:1, method :"norm.ihs.prop"]
Wrote counts and metadata for raw counts Normalized after default transformations to files data/1.1.1.4.2.2-3234196d035samples.raw.16s.l.otu.count.tsv,data/1.1.1.4.2.2-3234196d035samples.raw.16s.l.otu.attr.tsv
Count normalization method for abundance plots : [ drop.features:List of 1, ..$ :"other", method.args : list(), method :"norm.prop"]
(1.1.1.4.3) Figure 233. Clustered heatmap of normalized abundance values. Number of cluster splits is determined automatically with method fpc::pamk. Image file: plots/32341ce43f8.svg.
(1.1.1.4.3) G-test of independence between automatic cluster splits and attribute 'Sample.type'. Number of cluster splits is determined automatically with method fpc::pamk.
| Test statistic | X-squared df | P value |
|---|---|---|
| 13.64 | 8 | 0.0917 |
person) (????). morpheus: Interactive heat maps using 'morpheus.js' and 'htmlwidgets'. R package version 0.1.1.1, <URL: https://github.com/cmap/morpheus.R>.
(1.1.1.4.3) Widget 71. Dynamic Morpheus heatmap of normalized abundance values. It is available here through the link only because it can take a while to render for large datasets. This is very customizable. What you will see initially is just a default starting configuration. Explore its menus. Click to see HTML widget file in full window: ./1.1.1.4.3-3231e89fbe2Dynamic.Morpheus.hea.html
Wrote counts and metadata for raw counts Data used for heatmap with added row cluster splits (clustering by abundance profile) to files data/1.1.1.4.3-3237d61e776samples.raw.htmap.count.tsv,data/1.1.1.4.3-3237d61e776samples.raw.htmap.attr.tsv
(1.1.1.4.3) Figure 234. Clustered heatmap of diversity and normalized abundance values. Number of cluster splits is determined automatically with method fpc::pamk. Image file: plots/3231895e722.svg. 
(1.1.1.4.3) G-test of independence between automatic cluster splits and attribute 'Sample.type'. Number of cluster splits is determined automatically with method fpc::pamk.
| Test statistic | X-squared df | P value |
|---|---|---|
| 0.2963 | 1 | 0.5862 |
Wrote counts and metadata for raw counts Data used for heatmap with added row cluster splits (clustering by Renyi diversity indices) to files data/1.1.1.4.3-3236105dd4dsamples.raw.htmap.count.tsv,data/1.1.1.4.3-3236105dd4dsamples.raw.htmap.attr.tsv
Design: Rapporter Team © 2011-2014 | Backend: pander | License: AGPL3 or OSL | Styled with skeleton
